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Article: tRNA derived fragments:A novel player in gene regulation and applications in cancer.

Zhang, Shuangshuang / Yu, Xiuchong / Xie, Yaoyao / Ye, Guoliang / Guo, Junming

2023 Volume 13, Page(s) 1063930

Abstract: The heterogeneous species of tRNA-derived fragments (tRFs) with specific biological functions was recently identified. Distinct roles of tRFs in tumor development and viral infection, mediated through transcriptional and post-transcriptional regulation, ... ...

Abstract	The heterogeneous species of tRNA-derived fragments (tRFs) with specific biological functions was recently identified. Distinct roles of tRFs in tumor development and viral infection, mediated through transcriptional and post-transcriptional regulation, has been demonstrated. In this review, we briefly summarize the current literatures on the classification of tRFs and the effects of tRNA modification on tRF biogenesis. Moreover, we highlight the tRF repertoire of biological roles such as gene silencing, and regulation of translation, cell apoptosis, and epigenetics. We also summarize the biological roles of various tRFs in cancer development and viral infection, their potential value as diagnostic and prognostic biomarkers for different types of cancers, and their potential use in cancer therapy.
Language	English
Publishing date	2023-01-20
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1063930
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Article ; Online: Linc-ROR Regulates

Yu, Xiuchong / Ma, Xinyi / Jia, Yangtao / Wu, Xinxin / Yan, Zhilong

Cell transplantation

2023 Volume 32, Page(s) 9636897231178902

Abstract: Gastric cancer is the third leading cause of cancer-related deaths worldwide, and research on gastric cancer pathogenesis is fundamental. Long intergenic non-coding RNAs (lincRNAs) control cancer initiation and progression through several mechanisms, ... ...

Abstract	Gastric cancer is the third leading cause of cancer-related deaths worldwide, and research on gastric cancer pathogenesis is fundamental. Long intergenic non-coding RNAs (lincRNAs) control cancer initiation and progression through several mechanisms, with the competitive endogenous RNA (ceRNA) regulatory network being the most common. In this study,
MeSH term(s)	Humans ; Stomach Neoplasms/genetics ; Cytoplasm ; Cell Count ; Cell Proliferation/genetics ; MicroRNAs/genetics ; Octamer Transcription Factor-3 ; SOXB1 Transcription Factors/genetics
Chemical Substances	MicroRNAs ; POU5F1 protein, human ; Octamer Transcription Factor-3 ; SOX2 protein, human ; SOXB1 Transcription Factors ; MIRN145 microRNA, human
Language	English
Publishing date	2023-06-12
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1135816-6
ISSN	1555-3892 ; 0963-6897
ISSN (online)	1555-3892
ISSN	0963-6897
DOI	10.1177/09636897231178902
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Article ; Online: Transfer RNA-derived fragments as novel biomarkers of the onset and progression of gastric cancer.

Xie, Yaoyao / Zhang, Shuangshuang / Yu, Xiuchong / Ye, Guoliang / Guo, Junming

Experimental biology and medicine (Maywood, N.J.)

2023 Volume 248, Issue 13, Page(s) 1095–1102

Abstract: Gastric cancer (GC) is a particularly malignant disease; thus, early diagnosis and treatment are especially important. Transfer RNA-derived small RNAs (tsRNAs) have been implicated in the onset and progression of various cancers. Therefore, the aim of ... ...

Abstract	Gastric cancer (GC) is a particularly malignant disease; thus, early diagnosis and treatment are especially important. Transfer RNA-derived small RNAs (tsRNAs) have been implicated in the onset and progression of various cancers. Therefore, the aim of this study was to explore the role of tRF-18-79MP9P04 (previously named tRF-5026a) in the onset and progression of GC. Expression levels of tRF-18-79MP9P04 were quantified in gastric mucosa specimens of healthy controls and plasma samples of patients with different stages of GC. The results showed that plasma levels of tRF-18-79MP9P04 were significantly decreased in the early and advanced stages of GC. The results of the nucleocytoplasmic separation assay found that tRF-18-79MP9P04 was localized in the nuclei of GC cells. High-throughput transcriptome sequencing identified genes regulated by tRF-18-79MP9P04 in GC cells, and the function of tRF-18-79MP9P04 was predicted by bioinformatics. Collectively, the findings of this study suggest that tRF-18-79MP9P04 would be useful as non-invasive biomarker for early diagnosis of GC and is related to cornification, the type I interferon signaling pathway, RNA polymerase II activities, and DNA binding.
MeSH term(s)	Humans ; Stomach Neoplasms/diagnosis ; Stomach Neoplasms/genetics ; Stomach Neoplasms/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; Biomarkers
Chemical Substances	RNA, Transfer (9014-25-9) ; Biomarkers
Language	English
Publishing date	2023-06-30
Publishing country	England
Document type	Journal Article
ZDB-ID	4015-0
ISSN	1535-3699 ; 1525-1373 ; 0037-9727
ISSN (online)	1535-3699 ; 1525-1373
ISSN	0037-9727
DOI	10.1177/15353702231179415
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Article: Absolute quantification of a plasma tRNA-derived fragment for the diagnosis and prognosis of gastric cancer.

Zhang, Shuangshuang / Xie, Yaoyao / Yu, Xiuchong / Ge, Jiaxin / Ye, Guoliang / Guo, Junming

Frontiers in oncology

2023 Volume 13, Page(s) 1106997

Abstract: Background: The transition from a healthy gastric mucosa to gastric cancer is a multi-step process. Early screening can significantly improve the survival rate of gastric cancer patients. A reliable liquid biopsy for gastric cancer prediction is ... ...

Abstract	Background: The transition from a healthy gastric mucosa to gastric cancer is a multi-step process. Early screening can significantly improve the survival rate of gastric cancer patients. A reliable liquid biopsy for gastric cancer prediction is urgently needed and since tRNA-derived fragments (tRFs) are abundant in various body fluids, tRFs are possible new biomarkers for gastric cancer. Methods: A total of 438 plasma samples from patients with different gastric mucosal lesions as well as healthy individuals were collected. A specific reverse transcription primer, a forward primer, a reverse primer, and a TaqMan probe were designed. A standard curve was constructed and an absolute quantitation method was devised for detection of tRF-33-P4R8YP9LON4VDP in plasma samples of individuals with differing gastric mucosa lesions. Receiver operating characteristic curves were constructed to evaluate the diagnostic values of tRF-33-P4R8YP9LON4VDP for individual with differing gastric mucosa. A Kaplan-Meier curve was established to calculate the prognostic value of tRF-33-P4R8YP9LON4VDP for advanced gastric cancer patients. Finally, a multivariate Cox regression analysis was performed to assess the independent prognostic value of tRF-33-P4R8YP9LON4VDP for advanced gastric cancer patients. Results: A detection method for plasma tRF-33-P4R8YP9LON4VDP was successfully established. Levels of plasma tRF-33-P4R8YP9LON4VDP were shown to reflect a gradient change from healthy individuals to gastritis patients to early and advanced gastric cancer patients. Significant differences were found among individuals with differing gastric mucosa, with reduced levels of tRF-33-P4R8YP9LON4VDP significantly related to a poor prognosis. tRF-33-P4R8YP9LON4VDP was found to be an independent predictor of an unfavorable survival outcome. Conclusions: In this study, we developed a quantitative detection method for plasma tRF-33-P4R8YP9LON4VDP that exhibited hypersensitivity, convenience, and specificity. Detection of tRF-33-P4R8YP9LON4VDP was found to be a valuable means by which to monitor different gastric mucosa and to predict patient prognosis.
Language	English
Publishing date	2023-04-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2649216-7
ISSN	2234-943X
ISSN	2234-943X
DOI	10.3389/fonc.2023.1106997
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Article ; Online: Ailanthone suppresses the activity of human colorectal cancer cells through the STAT3 signaling pathway.

Ding, Haixiang / Yu, Xiuchong / Yan, Zhilong

International journal of molecular medicine

2021 Volume 49, Issue 2

Abstract: Ailanthone (AIL) is a major quassinoid extracted from the Chinese medicinal herb, ...

Abstract	Ailanthone (AIL) is a major quassinoid extracted from the Chinese medicinal herb,
MeSH term(s)	Apoptosis/drug effects ; Caspases/metabolism ; Cell Cycle Checkpoints/drug effects ; Cell Line, Tumor ; Cell Movement/drug effects ; Cell Proliferation/drug effects ; Colorectal Neoplasms/metabolism ; Colorectal Neoplasms/pathology ; Humans ; Janus Kinases/metabolism ; Mitochondria/drug effects ; Mitochondria/metabolism ; Models, Biological ; Quassins/chemistry ; Quassins/pharmacology ; STAT3 Transcription Factor/metabolism ; Signal Transduction/drug effects
Chemical Substances	Quassins ; STAT3 Transcription Factor ; STAT3 protein, human ; ailanthone (981-15-7) ; Janus Kinases (EC 2.7.10.2) ; Caspases (EC 3.4.22.-)
Language	English
Publishing date	2021-12-27
Publishing country	Greece
Document type	Journal Article
ZDB-ID	1444428-8
ISSN	1791-244X ; 1107-3756
ISSN (online)	1791-244X
ISSN	1107-3756
DOI	10.3892/ijmm.2021.5076
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Article ; Online: tRNA-derived fragments: Mechanisms underlying their regulation of gene expression and potential applications as therapeutic targets in cancers and virus infections.

Yu, Xiuchong / Xie, Yaoyao / Zhang, Shuangshuang / Song, Xuemei / Xiao, Bingxiu / Yan, Zhilong

Theranostics

2021 Volume 11, Issue 1, Page(s) 461–469

Abstract: tRNA-derived fragments (tRFs) are a new category of regulatory noncoding RNAs with distinct biological functions in cancers and stress-induced diseases. Herein, we first summarize the classification and biogenesis of tRFs. tRFs are produced from pre- ... ...

Abstract	tRNA-derived fragments (tRFs) are a new category of regulatory noncoding RNAs with distinct biological functions in cancers and stress-induced diseases. Herein, we first summarize the classification and biogenesis of tRFs. tRFs are produced from pre-tRNAs or mature tRNAs. Based on the incision loci, tRFs are classified into several types: tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF. Some tRFs participate in posttranscriptional regulation through microRNA-like actions or by displacing RNA binding proteins and regulating protein translation by promoting ribosome biogenesis or interfering with translation initiation. Other tRFs prevent cell apoptosis by binding to cytochrome
MeSH term(s)	Apoptosis/genetics ; Gene Expression Regulation ; Gene Expression Regulation, Neoplastic ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Protein Biosynthesis/genetics ; RNA Precursors/genetics ; RNA Precursors/metabolism ; RNA Stability/genetics ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; RNA-Binding Proteins/metabolism ; Virus Diseases/genetics ; Virus Diseases/metabolism ; Virus Replication
Chemical Substances	RNA Precursors ; RNA, Small Untranslated ; RNA-Binding Proteins ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2021-01-01
Publishing country	Australia
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2592097-2
ISSN	1838-7640 ; 1838-7640
ISSN (online)	1838-7640
ISSN	1838-7640
DOI	10.7150/thno.51963
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Article ; Online: Global profile of tRNA-derived small RNAs in gastric cancer patient plasma and identification of tRF-33-P4R8YP9LON4VDP as a new tumor suppressor.

Shen, Yijing / Yu, Xiuchong / Ruan, Yao / Li, Zhe / Xie, Yaoyao / Yan, Zhilong / Guo, Junming

International journal of medical sciences

2021 Volume 18, Issue 7, Page(s) 1570–1579

Abstract: Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have been found to play important roles in the occurrence and development of cancers. However, the tsRNA profile in gastric cancer is unknown. In this study, we aimed to identify the global tsRNA profile in ...

Abstract	Transfer RNA (tRNA)-derived small RNAs (tsRNAs) have been found to play important roles in the occurrence and development of cancers. However, the tsRNA profile in gastric cancer is unknown. In this study, we aimed to identify the global tsRNA profile in plasma from gastric cancer patients and elucidate the role of tRF-33-P4R8YP9LON4VDP in gastric cancer. Differentially expressed tsRNAs in the plasma of gastric cancer patients and healthy controls were investigated using RNA sequencing. The expression levels of tRF-33-P4R8YP9LON4VDP in the plasma of gastric cancer patients, healthy controls and gastric cancer cell lines were first detected by quantitative reverse transcription-polymerase chain reaction. The effects of tRF-33-P4R8YP9LON4VDP overexpression or downregulation in gastric cancer cells on proliferation, migration, apoptosis, and cell cycle were analyzed using the Cell Counting Kit-8, scratch assay, Transwell assay, and flow cytometry, respectively. There were 21 upregulated and 46 downregulated tsRNAs found in plasma from gastric cancer patients. The significantly upregulated tsRNAs included tRF-18-S3M83004, tRF-31-PNR8YP9LON4VD, tRF-19-3L7L73JD, tRF-33-P4R8YP9LON4VDP, tRF-31-PER8YP9LON4VD, tRF-18-MBQ4NKDJ, and tRF-31-PIR8YP9LON4VD. The significantly downregulated tsRNAs included tRF-41-YDLBRY73W0K5KKOVD, tRF-18-07QSNHD2, tRF-28-86J8WPMN1E0J, tRF-29-86V8WPMN1EJ3, tRF-31-6978WPRLXN4VE, tRF-30-MIF91SS2P46I, tRF-26-MI7O3B1NR8E, tRF-30-RRJ89O9NF5W8, tRF-26-XIP2801MK8E, and tRF-35-V0J8O9YEKPRS93,
MeSH term(s)	Biomarkers, Tumor/genetics ; Biomarkers, Tumor/metabolism ; Carcinoma/blood ; Carcinoma/diagnosis ; Carcinoma/genetics ; Carcinoma/surgery ; Cell Proliferation/genetics ; Down-Regulation ; Gastrectomy ; Gastric Mucosa/pathology ; Gastric Mucosa/surgery ; Gene Expression Regulation, Neoplastic ; Genes, Tumor Suppressor ; Humans ; Liquid Biopsy/methods ; RNA, Small Untranslated/genetics ; RNA, Small Untranslated/metabolism ; RNA, Transfer/genetics ; RNA-Seq ; Stomach Neoplasms/blood ; Stomach Neoplasms/diagnosis ; Stomach Neoplasms/genetics ; Stomach Neoplasms/surgery ; Up-Regulation
Chemical Substances	Biomarkers, Tumor ; RNA, Small Untranslated ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2021-02-04
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2151424-0
ISSN	1449-1907 ; 1449-1907
ISSN (online)	1449-1907
ISSN	1449-1907
DOI	10.7150/ijms.53220
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Article: Clinical diagnostic values of transfer RNA-derived fragment tRF-19-3L7L73JD and its effects on the growth of gastric cancer cells.

Shen, Yijing / Xie, Yaoyao / Yu, Xiuchong / Zhang, Shuangshuang / Wen, Qiuyan / Ye, Guoliang / Guo, Junming

Journal of Cancer

2021 Volume 12, Issue 11, Page(s) 3230–3238

Abstract: Background and aim: ...

Abstract	Background and aim:
Language	English
Publishing date	2021-04-02
Publishing country	Australia
Document type	Journal Article
ZDB-ID	2573318-7
ISSN	1837-9664
ISSN	1837-9664
DOI	10.7150/jca.51567
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Article ; Online: Extracellular vesicles-associated tRNA-derived fragments (tRFs): biogenesis, biological functions, and their role as potential biomarkers in human diseases.

Weng, Qiuyan / Wang, Yao / Xie, Yaoyao / Yu, Xiuchong / Zhang, Shuangshuang / Ge, Jiaxin / Li, Zhe / Ye, Guoliang / Guo, Junming

Journal of molecular medicine (Berlin, Germany)

2022 Volume 100, Issue 5, Page(s) 679–695

Abstract: Traditionally, transfer RNAs (tRNAs) specifically decoded messenger RNA (mRNA) and participated in protein translation. tRNA-derived fragments (tRFs), also known as tRNA-derived small RNAs (tsRNAs), are generated by the specific cleavage of pre- and ... ...

Abstract	Traditionally, transfer RNAs (tRNAs) specifically decoded messenger RNA (mRNA) and participated in protein translation. tRNA-derived fragments (tRFs), also known as tRNA-derived small RNAs (tsRNAs), are generated by the specific cleavage of pre- and mature tRNAs and are a class of newly defined functional small non-coding RNAs (sncRNAs). Following the different cleavage positions of precursor or mature tRNA, tRFs are classified into seven types, 5'-tRNA half, 3'-tRNA half, tRF-1, 5'U-tRF, 3'-tRF, 5'-tRF, and i-tRF. It has been demonstrated that tRFs have a diverse range of biological functions in cellular processes, which include inhibiting protein translation, modulating stress response, regulating gene expression, and involvement in cell cycles and epigenetic inheritance. Emerging evidences have indicated that tRFs in extracellular vesicles (EVs) seem to act as regulatory molecules in various cellular processes and play essential roles in cell-to-cell communication. Furthermore, the dysregulation of EV-associated tRFs has been associated with the occurrence and progression of a variety of cancers and they can serve as novel potential biomarkers for cancer diagnosis. In this review, the biogenesis and classification of tRFs are summarized, and the biological functions of EV-associated tRFs and their roles as potential biomarkers in human diseases are discussed.
MeSH term(s)	Biomarkers/metabolism ; Extracellular Vesicles/metabolism ; Humans ; Neoplasms/genetics ; Neoplasms/metabolism ; Protein Biosynthesis ; RNA, Transfer/genetics ; RNA, Transfer/metabolism
Chemical Substances	Biomarkers ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2022-03-24
Publishing country	Germany
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	1223802-8
ISSN	1432-1440 ; 0946-2716
ISSN (online)	1432-1440
ISSN	0946-2716
DOI	10.1007/s00109-022-02189-0
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Ua VI Zs.36: Show issues

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Article ; Online: Action mechanisms and research methods of tRNA-derived small RNAs.

Xie, Yaoyao / Yao, Lipeng / Yu, Xiuchong / Ruan, Yao / Li, Zhe / Guo, Junming

Signal transduction and targeted therapy

2020 Volume 5, Issue 1, Page(s) 109

Abstract: tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by ... ...

Abstract	tRNA-derived small RNAs (tsRNAs), including tRNA-derived fragments (tRFs) and tRNA halves (tiRNAs), are small regulatory RNAs processed from mature tRNAs or precursor tRNAs. tRFs and tiRNAs play biological roles through a variety of mechanisms by interacting with proteins or mRNA, inhibiting translation, and regulating gene expression, the cell cycle, and chromatin and epigenetic modifications. The establishment and application of research technologies are important in understanding the biological roles of tRFs and tiRNAs. To study the molecular mechanisms of tRFs and tiRNAs, researchers have used a variety of bioinformatics and molecular biology methods, such as microarray analysis, real-time quantitative reverse transcription-polymerase chain reaction (qRT-PCR); Northern blotting; RNA sequencing (RNA-seq); cross-linking, ligation and sequencing of hybrids (CLASH); and photoactivatable-ribonucleoside-enhanced cross-linking and immunoprecipitation (PAR-CLIP). This paper summarizes the classification, action mechanisms, and roles of tRFs and tiRNAs in human diseases and the related signal transduction pathways, targeted therapies, databases, and research methods associated with them.
MeSH term(s)	Animals ; Cell Cycle ; Cell Proliferation ; Epigenesis, Genetic ; Humans ; RNA, Transfer/metabolism ; RNA-Seq ; Signal Transduction
Chemical Substances	RNA, Transfer (9014-25-9)
Language	English
Publishing date	2020-06-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2886872-9
ISSN	2059-3635 ; 2095-9907
ISSN (online)	2059-3635
ISSN	2095-9907
DOI	10.1038/s41392-020-00217-4
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